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Bioinformatics analysis of epitope-based vaccine design against the novel SARS-CoV-2

Infectious diseases of Poverty 2020年第4期9卷 169-169页

作者： Hong-Zhi Chen Ling-Li Tang Xin-Ling Yu Jie Zhou Yun-Feng Chang Xiang Wu Department of Metabolism&Endocrinology Metabolic Syndrome Research CenterKey Laboratory of Diabetes ImmunologyMinistry of EducationNational Clinical Research Center for Metabolic DiseaseThe Second Xiangya HospitalCentral South UniversityChangsha410011HunanChina Department of Laboratory Medicine The Second Xiangya HospitalCentral South UniversityChangsha410011HunanChina Hunan Institute of Parasite disease WHO Collaborating Center For Research and Control on Schistosomiasis in Lake RegionYueyang414000HunanChina Department of Forensic Medicine Science Xiangya School of Basic MedicineCentral South UniversityChangsha410013HunanChina Department of Parasitology Xiangya School of Basic MedicineCentral South UniversityChangsha410013HunanChina

Background An outbreak of infection caused by SARS-CoV-2 recently has brought a great challenge to public *** identification of immune epitopes would be an efficient way to screen the candidates for vaccine development at the time of *** study aimed to predict the protective epitopes with bioinformatics methods and resources for vaccine *** The genome sequence and protein sequences of SARS-CoV-2 were retrieved from the National center for Biotechnology Information(NCBI)*** and BepiPred servers were utilized for sequential B-cell epitope *** B-cell epitopes were predicted via DiscoTope 2.0 *** server was utilized for HLA-1 and HLA-2 binding peptides *** accessibility,antigenicity,and other important features of forecasted epitopes were characterized for immunogen potential *** A total of 63 sequential B-cell epitopes on spike protein were predicted and 4 peptides(Spike315–324,Spike333–338,Spike648–663,Spike1064–1079)exhibited high antigenicity score and good surface *** residues within spike protein(Gly496,Glu498,Pro499,Thr500,Leu1141,Gln1142,Pro1143,Glu1144,Leu1145,Asp1146)are forecasted as components of discontinuous B-cell *** bioinformatics analysis of HLA binding peptides within nucleocapsid protein produced 81 and 64 peptides being able to bind MHC class I and MHC class II molecules *** peptides(Nucleocapsid66–75,Nucleocapsid104–112)were predicted to bind a wide spectrum of both HLA-1 and HLA-2 *** B-cell epitopes on spike protein and T-cell epitopes within nucleocapsid protein were identified and recommended for developing a protective vaccine against SARS-CoV-2.

关键词： SARS-CoV-2 Epitope Vaccine Bioinformatics

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Effects of Dietary Supplementation with Cysteamine on Performance, Carcass Characteristics, Meat Quality and Antioxidant Status in Finishing Pigs

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Journal of Agricultural Science and Technology 2011年第1期5卷 14-19页

作者： X. Z. Lv Y. Wang G. L. Liu Z. S. Wang A. G. Zhou Institute of Animal Nutrition Sichuan Agricultural University Ya ＇an 625014 Sichuan China Engineering Research center of Animal disease-Resistance Nutrition of China Ministry of Education Ya＇an 625014 SichuanChina

The current study was to investigate the effects of cysteamine （CS） on carcass characteristics, meat quality, and antioxidant status in finishing pigs. A total of 24 crossbred （PIC variety） finishing pigs （60.05±1.24 kg, 12 gilts and 12 barrows） were assigned randomly to one of the three dietary groups, with four pens/group （one gilt and one barrow per pen）. Pigs were fed with a basal diet containing 0 （control）, 70, or 140 mg/kg CS for 47 days. The results indicated that dietary CS supplementation increased （P〈0.05） the average daily gain and feed intake with optimal responses occurring at 70 mg/kg. Dietary supplementation of CS increased （P〈0.05） the dressing percentage and lean percentage of finishing pigs with optimal responses occurring at 140 mg/kg. The CS supplementation, however, had no effect （P〉0.05） on meat quality. Dietary CS supplementation increased （P〈0.05） total antioxidant capacity （T-AOC） and decreased malondialdehyde （MDA） with optimal responses occurring at 70 mg/kg. CS supplementation at both 70 mg/kg and 140 mg/kg doses improved （P〈0.05） the muscle RNA/DNA ratio. Collectively, the results suggest dietary supplementation of 70 mg/kg CS could significantly improve growth performance and antioxidant status without adverse effects on the gastrointestinal tracts in finishing pigs while the 140 mg/kg CS supplementation improved the carcass quality. However, meat quality was not affected by CS supplementation.

关键词： Cysteamine growth carcass characteristics meat quality antioxidant status finishing pigs.

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Automated generation and ensemble-learned matching of X-ray absorption spectra

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npj Computational Materials 2018年第1期4卷 566-574页

作者： Chen Zheng Kiran Mathew Chi Chen Yiming Chen Hanmei Tang Alan Dozier Joshua J.Kas Fernando D.Vila John J.Rehr Louis F.J.Piper Kristin A.Persson Shyue Ping Ong Department of NanoEngineering University of California San Diego9500 Gilman DriveMail Code 0448La JollaCA 92093-0448USA Department of Materials Science University of California BerkeleyBerkeleyCA 94720USA Division of Applied Research and Technology National Institute for Occupational Safety and HealthCenters for Disease ControlCincinnatiOH 45226USA Department of Physics University of WashingtonSeattleWA 98195USA Department of Physics Applied Physics and AstronomyBinghamton UniversityBinghamtonNY 13902USA Materials Science&Engineering Binghamton UniversityBinghamtonNY 13902USA

X-ray absorption spectroscopy(XAS)is a widely used materials characterization technique to determine oxidation states,coordination environment,and other local atomic structure *** of XAS relies on comparison of measured spectra to reliable reference ***,existing databases of XAS spectra are highly limited both in terms of the number of reference spectra available as well as the breadth of chemistry *** this work,we report the development of XASdb,a large database of computed reference XAS,and an Ensemble-Learned Spectra IdEntification(ELSIE)algorithm for the matching of *** currently hosts more than 800,000 K-edge X-ray absorption near-edge spectra(XANES)for over 40,000 materials from the open-science Materials Project *** discuss a high-throughput automation framework for FEFF calculations,built on robust,rigorously benchmarked *** is a computer program uses a real-space Green’s function approach to calculate X-ray absorption *** will demonstrate that the ELSIE algorithm,which combines 33 weak“learners”comprising a set of preprocessing steps and a similarity metric,can achieve up to 84.2% accuracy in identifying the correct oxidation state and coordination environment of a test set of 19 K-edge XANES spectra encompassing a diverse range of chemistries and crystal *** XASdb with the ELSIE algorithm has been integrated into a web application in the Materials Project,providing an important new public resource for the analysis of XAS to all materials ***,the ELSIE algorithm itself has been made available as part of veidt,an open source machine-learning library for materials science.

关键词： matching XANES ensemble

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QTL mapping of adult-plant resistance to leaf rust in Romanian wheat line Fundulea 900

QTL mapping of adult-plant resistance to leaf rust in Romani...

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中国植物病理学会2015年学术年会

作者： ZHANG Pei-pei LI Qing-luo WANG Xin-hai LI Zai-feng LIU Da-qun College of Plant Protection Hebei Agricultural UniversityBiological Control Center for Plant Diseases and Plant Pests of Hebei

Wheat leaf rust is a destructive worldwide foliar disease of common wheat(Triticum aestivum L.).The most effective,economic means to control the disease is planting resistant cultivars with adult plant resistance(APR).The Romanian wheat line Fundulea 900 showed high leaf rust resistance in the *** identify leaf rust APR genes in Fundulea 900,the mapping populations with 188 Flines from the cross Fundulea 900/Thatcher was phenotyped for leaf rust severities during the2010-2011,2011-2012 and 2012—2013 cropping seasons in the field at Baoding,Hebei province.A total of 1,215 SSR markers were used to identify the quantitative trait loci(QTL) for leaf rust APR in the *** the Fundulea 900/Thatcher population,three QTL were detected,and designated as ***-1BL,***-2DS and *** on chromosome positions and molecular marker tests,***-lBL is Lr46,and ***-TDS is ***-2DS mapped on chromosome 2DS might be a new *** QTL and their closely linked markers are potentially useful for improving leaf rust resistance in wheat breeding.

关键词： Triticum aestivum Puccinia triticina APR SSR marker

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Oral health status of Chinese residents and suggestions for prevention and treatment strategies

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Global Health Journal 2019年第2期3卷 50-54页

作者： Yan Si Baoiun Tai Deyu Hu Huancai Lin Bo Wang Chunxiao Wang Shuguo Zheng Xuenan Liu Wensheng Rong Weijian Wang Xiping Feng Xing Wang Department of Preventive Dentistry Peking University Hospital of Stamatology22Zhongguancun South AvenueHaidian DistrictBeijing100081China Peking University School of Stamatology 22Zhongguancun South AvenueHaidian DistrictBeijing100081China National Engineering Laboratory for Digital and Material Technology of Stomatology 22Zhongguancun South AvenueHaidian DistrictBeijing100081China Beijing Key Laboratory of Digital Stomatology 22Zhongguancun South AvenueHaidian DistrictBeijing100081China Department of Preventive Dentistry Hospital of Stomatology Wuhan University237Luoyu RoadHongshan DistrictWuhan430079China The State Key Laboratory Breeding Base of Basic Science of Stomatology Hubei Province Key Laboratory of Oral Biomedicine Ministry of EducationWuhan University237Luoyu RoadHongshan DistrictWuhan430079China Department of Preventive Dentistry West China School/Hospital of StomatologySichuan University14the Third Section of Renming South Streetchengdu610041China Department of Preventive Dentistry Guanghua School of StomatologyHospital of StomatologySun Yat-Sen University56Cemetery West StreetGuangzhou510055China Guangdong Provincial Key Laboratory of Stomatology 56Cemetery West StreetGuangzhou510055China Chinese Stomatological Association Jia-18Zhongguancun South AvenueHaidian DistrictBeijing100081China center for Chronic and Non-communicable disease control and prevention Chinese Center for Disease Control and Prevention27Nanwei RoadWest City DistrictBeijing100050China Department of Preventive Dentistry Shanghai Ninth People's HospitalShanghai JiaoTong University School of Medicine639Manufacturing Bureau RoadShanghai200011China Shanghai Key Laboratory of Stomatology 639Manufacturing Bureau RoadShanghai200011China

Objective:To understand the oral health status of urban and rural residents in China,the Fourth National Oral Health Epidemiological Survey (FNOHES) was conducted in *** and methods:Based on the principles of multi-stage,stratified,equal capacity,and random sampling,the subjects included five groups of residents aged 3-5,12-15,35-44,55-64,and 65-74 years in all 31 provinces,municipalities,and autonomous regions except Hong Kong,Macao,and *** total sample size was 172,*** survey covered two areas,namely oral health status and knowledge,attitude and oral health ***:Residents in China had serious caries and poor periodontal *** prevalence of caries was above 50% in all age groups,subjects without periodontal disease accounted for prevention and control system for oral diseases,implement a comprehensive prevention and control strategy for priority groups,strengthen the oral health education for all people to improve oral health literacy,enhance dynamic monitoring to scientifically evaluate oral health status,and coordinate multi-party resources to establish and improve the oral health service security ***:The oral health status of Chinese residents and their oral health behavior habits need to be *** the support of the administrative departments of the government and unremitting efforts of the oral health staff,all sectors of society must be coordinated to strengthen oral health education for the whole ***,comprehensive prevention and control measures must be implemented for priority groups.

关键词： Caries Periodontitis Oral health Oral disease Epidemiological study Comprehensive prevention and control The Fourth National Oral Health Epidemiological Survey

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Screening of chemokine receptor CCR4 antagonists by capillary zone electrophoresis

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Journal of Pharmaceutical Analysis 2011年第4期1卷 264-269页

作者： Zhe Sun Lin-Jie Tian Qian Lin Xiao-Mei Ling Jun-Hai Xiao Ying Wang Department of Pharmaceutical Analysis of School of Pharmaceutical Sciences and State Key Laboratory of Natural andBiomimetic Drugs Peking University Beijing 100191 PR China center for Human disease Genomics and Department of Medical Immunology of School of Basic Medical SciencePeking University Beijing 100191 PR China Beijing Institute of Pharmacology and Toxicology Beijing 100850 PR China

Abstract CC chemokine receptor 4 （CCR4） is a kind of G-protein-coupled receptor, which plays a pivotal role in allergic inflammation. The interaction between 2-（2-（4-chloro-phenyl）-5-{[（naphthalen-1- ylmethyl）-carbamlyl]-methyl-4-oxo-thiazolidin-3-yl）-N-（3-morpholin-4-yl-propyi）-acetamide （S009） and the N-terminal extracellular tail （ML40） of CCR4 has been validated to be high affinity by capillary zone electrophoresis （CZE）.The S009 is a known CCR4 antagonist. Now, a series of new thiourea derivatives have been synthesized. Compared with positive control S009, they were screened using ML40 as target by CZE to find some new drugs for allergic inflammation diseases. The synthesized compounds XJH-5, XJH-4, XJH-17 and XJH-1 displayed the interaction with ML40, but XJH-9, XJH-10, XJH-I 1, XJH-12, XJH-13, XJH-14, XJH-3, XJH-8, XJH-6, XJH-7, XJH-15, XJH-16 and XJH-2 did not bind to ML40. Both qualification and quantification characterizations of the binding were determined. The affinity of the four compounds was valued by the binding constant, which was similar with the results of chemotactic experiments. The established CEZ method is capable of sensitive and fast screening for a series of lactam analogs in the drug discovery for allergic inflammation diseases.

关键词： Capillary zoneelectrophoresis CCR4 antagonist 2-(2-(4-chloro-phenyl)-5-{[(naphthalen- 1-ylmethyl)-carbamoyl]-methyl} -4-oxo-thiazoli-din-3-yl)-N-(3-morpho-lin-4-yl-propyl)-aceta-mide Interactions Structural modification

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A Naive Bayes model on lung adenocarcinoma projection based on tumor microenvironment and weighted gene coexpression network analysis

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Infectious disease Modelling 2022年第3期7卷 498-509页

作者： Zhiqiang Ye Pingping Song Degao Zheng Xu Zhang Jianhong Wu School of Elementary Education Chongqing Normal UniversityChongqing400700China School of Mathematics and Statistics Southwest UniversityChongqing400715China Chongqing Experimental High School Chongqing401320China Laboratory for Industrial and Applied Mathematics Center for Disease ModellingYork UniversityTorontoONM3J 1P3Canada

Based on the lung adenocarcinoma(LUAD)gene expression data from the cancer genome atlas(TCGA)database,the Stromal score,Immune score and Estimate score in tumor microenvironment(TME)were computed by the Estimation of Stromal and Immune cells in Malignant Tumor tissues using Expression data(ESTIMATE)*** gene modules significantly related to the three scores were identified by weighted gene coexpression network analysis(WGCNA).Based on the correlation coefficients and P values,899 key genes affecting tumor microenvironment were obtained by selecting the two most correlated *** was suggested through Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analysis that these key genes were significantly involved in immune-related or cancer-related *** univariate cox regression and elastic network analysis,genes associated with prognosis of the LUAD patients were screened out and their prognostic values were further verified by the survival analysis and the University of ALabama at Birmingham CANcer(UALCAN)*** results indicated that eight genes were significantly related to the overall survival of *** them,six genes were found differentially expressed between tumor and control *** immune infiltration analysis further verified that all the six genes were significantly related to tumor purity and immune ***,these genes were used eventually for constructing a Naive Bayes projection model of *** model was verified by the receiver operating characteristic(ROC)curve where the area under curve(AUC)reached 92.03%,which suggested that the model could discriminate the tumor samples from the normal *** study provided an effective model for LUAD projection which improved the clinical diagnosis and cure of *** result also confirmed that the six genes in the model construction could be the potential prognostic biomarkers of LUAD.

关键词： Naive Bayes model Tumor microenvironment Lung adenocarcinoma Weighted gene co-expression network analysis Prognostic biomarkers

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Molecularly specific detection of bacterial lipoteichoic acid for diagnosis of prosthetic joint infection of the bone

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Bone Research 2018年第2期6卷 189-196页

作者： Julie E.Pickett John M.Thompson Agnieszka Sadowska Christine Tkaczyk Bret R.Sellman Andrea Minola Davide Corti Antonio Lanzavecchia Lloyd S.Miller Daniel LJ Thorek Division of Nuclear Medicine and Molecular Imaging Department of Radiology and Radiological ScienceJohns Hopkins University School of MedicineGaithersburgMDUSA Department of Orthopaedic Surgery Johns Hopkins University School of MedicineBaltimoreMD 21205USA Department of Infectious disease MedImmune LLCGaithersburgMDUSA Humabs Bio Med SA BellinzonaSwitzerland Institute for Research in Biomedicine Universitàdella Svizzera italianaBellinzonaSwitzerland Department of Dermatology Johns Hopkins University School of MedicineBaltimoreMD 21205USA Division of Infectious disease Department of MedicineJohns Hopkins University School of MedicineBaltimoreMDUSA Cancer Molecular and Functional Imaging Program Department of OncologySidney Kimmel Comprehensive Cancer CenterJohns Hopkins University School of MedicineBaltimoreMD 21205USA

Discriminating sterile inflammation from infection, especially in cases of aseptic loosening versus an actual prosthetic joint infection, is challenging and has significant treatment implications. Our goal was to evaluate a novel human monoclonal antibody（mAb） probe directed against the Gram-positive bacterial surface molecule lipoteichoic acid（LTA）. Specificity and affinity were assessed in vitro. We then radiolabeled the anti-LTA mAb and evaluated its effectiveness as a diagnostic imaging tool for detecting infection via immuno PET imaging in an in vivo mouse model of prosthetic joint infection（PJI）. In vitro and ex vivo binding of the anti-LTA mAb to pathogenic bacteria was measured with Octet, ELISA, and flow cytometry. The in vivo PJI mouse model was assessed using traditional imaging modalities, including positron emission tomography（PET） with [^（18）F]FDG and [^（18）F]Na F as well as X-ray computed tomography（CT）, before being evaluated with the zirconium-89-labeled antibody specific for LTA（[^（89）Zr]SAC55）.The anti-LTA mAb exhibited specific binding in vitro to LTA-expressing bacteria. Results from imaging showed that our model could reliably simulate infection at the surgical site by bioluminescent imaging, conventional PET tracer imaging, and bone morphological changes by CT. One day following injection of both the radiolabeled anti-LTA and isotype control antibodies, the anti-LTA antibody demonstrated significantly greater（P 〈 0.05） uptake at S. aureus-infected prosthesis sites over either the same antibody at sterile prosthesis sites or of control non-specific antibody at infected prosthesis sites. Taken together, the radiolabeled anti-LTA mAb, [^（89）Zr]SAC55, may serve as a valuable diagnostic molecular imaging probe to help distinguish between sterile inflammation and infection in the setting of PJI. Future studies are needed to determine whether these findings will translate to human PJI.

关键词： Zr Molecularly specific detection bacterial lipoteichoic acid diagnosis prosthetic infection bone LTA SAC PET FDG tracer

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Different strategies for ultra-early reperfusion therapy in anterior circulation acute ischemic stroke safety and effectiveness of the comparative observation

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Clinical Research Communications 2023年第2期6卷 33-38页

作者： Wen-Jing Zhou Lu Yang Yan-Chao Huo Meng Geng Meng Zhang Chuan-Hui Li Na Shang Yao-Ming Xu Department of Neurology Tongliao City HospitalTongliao 028000China Tongliao Clinical Medical College Inner Mongolia Medical UniversityTongliao 028000China Emergency Department Xuanwu HospitalCapital Medical UniversityBeijing 100032China Department of Chronic disease Management and control Tongliao Municipal Center for Disease Control and PreventionTongliao 028000China.

Background:To compare the safety and effectiveness of direct mechanical thrombectomy and bridging therapy for stroke with acute anterior circulation large vessel occlusion within 4.5 hours of ***:Retrospectively collected from 66 patients with acute ischemic stroke admitted to the Department of Neurology of Tongliao Hospital and Xuanwu Hospital from August 2019 to November 2021 within 4.5 *** to the different recanalization methods,30 patients were assigned to the direct thrombectomy treatment group,and 36 patients in the bridging treatment group(i.e.,the intravenous thrombolysis bridging mechanical thrombectomy treatment group).The primary outcome measure was the neurological outcome at the onset of *** outcome measures were intraoperative vascular recanalization and reperfusion,and the US National Institute of Health Stroke Scale score at 24 hours after *** primary safety indicators are intracranial hemorrhage,including symptomatic intracranial hemorrhage and non-symptomatic intracranial hemorrhage,and 90d ***:The direct thrombectomy group had lower body mass index,hypertension and baseline Alberta early computed tomography score than the bridging treatment group,and longer time from onset to visit than the bridging group(206.5(119.5,256.25)min vs.150.5(25.205,212.75)min),the above difference were statistically significant(P0.05).Conclusion:Similar clinical efficacy and safety of direct mechanical thrombectomy and bridging therapy for acute anterior circulation large vessel occlusive stroke within 4.5 hours of onset,direct thrombectomy can be used as an alternative scheme for acute anterior

关键词： anterior circulation direct thrombectomy therapy bridging therapy intracranial large vessel occlusion acute ischemic stroke

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Protective effect of hydroxychloroquine on rheumatoid arthritis-associated atherosclerosis

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Animal Models and Experimental Medicine 2019年第2期2卷 98-106页

作者： Na Shi Shuangyue Zhang Gregg Silverman Mengtao Li Jun Cai Haitao Niu NHC Key Laboratory of Human disease Comparative Medicine (The Institute of Laboratory Animal Sciences CAMS&PUMC) Key Laboratory of Human Diseases Animal Model State Administration of Traditional Chinese Medicine Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases Beijing China Department of Rheumatology Langone Medical Center New York University New York City New York Peking Union Medical College Hospital Beijing China Fuwai Hospital Chinese Academy of Medical Sciences Beijing China

Background: Patients with rheumatoid arthritis (RA) have an increased risk for cardiovascular disease. We examined the effect of gut microbiota in a mouse model of RA that develops atherosclerosis. Methods: We created three groups of K/BxN female mice that were positive for the anti‐glucose‐6‐phosphate isomerase (GPI) antibody: control diet (CD), high fat diet (HFD), and HFD with hydroxychloroquine (HFD + HCQ). Serological tests were used to detect the serum levels of total cholesterol (TCHO), low‐density lipoprotein cholesterol (LDL‐C), triglyceride (TG), high‐density lipoprotein cholesterol (HDL‐C), anti‐ GPI antibody titers, and serum cytokines. Atherosclerotic plaque was determined by histological analysis, and gut microbiota were determined by 16sV4 sequencing. Results: Relative to mice given the CD, those receiving the HFD had increased serum levels of LDL‐C, TCHO, and TG, decreased serum levels of HDL‐C, increased atherosclerotic lesions in the aortic root, and altered gut microbiota. Addition of HCQ to HFD decreased the serum levels of LDL‐C, TCHO, and TG, increased serum levels of HDL‐C, and decreased the atherosclerotic lesions in the aortic root. Mice receiving HFD + HCQ also had the greatest bacterial diversity among the three experimental groups. Moreover, HCQ treatment significantly increased the abundance of Akkermansia and Parabacteroides, and decreased the abundance of Clostridium sensu stricto cluster 1, and therefore may be responsible for the reduced RA‐associated atherosclerosis and dyslipidemia. Conclusion: Our mouse model of RA indicated that HFD increased ankle width and aggravated a therosclerosis a nd d yslipidemia, a nd t hat H CQ a lleviated t he d yslipidemia and atherosclerosis, but had no effect on ankle width.

关键词： atherosclerosis autoimmunity hydroxychloroquine intestinal microbiota rheumatoid arthritis

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